About free-form database

[Francesco Pietra-2]

As a natural product chemist, memorizing data and chemical structures
is routine in my job. Aside the brain, I was using a free-form
database (which also allowed definition of flelds on-the-fly) driven
through the emulation program 'wine'. In writing books it was of
tremendous help.

Since I updated to lenny, wine is no more (or I am not) capable of
running the engine. 15 days of frequents attempts (purging everything
and reinstalling) could not solve the issue.

I never moved to structured database as I preferred to use the
database as a paper notebook, addressing the linking to the brain.
I.e, it was nothing different from the traditional way we are used to
study and follow the literature. Now I am forced to change, and I was
also tired to follow the vagaries of wine. I thought to SQLite as the
lightest alternative. I found it heavily structured. Not the way I am
used in learning and planning.

Therefore, I thought why not turning to 'grep' and  and perhaps also
'wc' and other commands for processing text. I have a text file
exported some time ago, the largest one of my databases (about marine
natural products) and I am (for the time being) extremely impressed by
the capability of grep. I can even retrieve - without fields - which
marine organisms have been collected (for natural product extraction)
between, say, 15 and 25m depth (a data retrieval that was only allowed
by the wine-driven database through fields.

Well, enthusiasm if often momentary. Before embarking with grep and
allies, I wonder whether there is established experience with what I
have described. That would help indeed.

Thanks

francesco pietra


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[Dirk Eddelbuettel]

This is a debian-user question.  Learn to use 'apt-cache search' --
there must be at least a hundred packages in Debian for what you
describe, from note taking to mind mappming to personal wikis.

Don't abuse debian-science because you think of yourself as a scientist.

Dirk

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[Ethan Romander]

On Mon, 2008-06-09 at 17:18 +0200, Francesco Pietra wrote:
> Well, enthusiasm if often momentary. Before embarking with grep and
> allies, I wonder whether there is established experience with what I
> have described. That would help indeed.

I use a small wiki for my journalling.  I started out with a tiddlywiki
and have since moved up to a moinmoin wiki.  Both are light weight wikis
(neither requires a webserver or database backend).  Moinmoin has better
support for embedded content (images, math, etc.).  Both can be
searched, but only using typical text searches---perhaps not enough
horsepower for your application.

Cheers.

--Ethan


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[Adam C Powell IV]

On Mon, 2008-06-09 at 15:29 +0000, Dirk Eddelbuettel wrote:
> This is a debian-user question.  Learn to use 'apt-cache search' --
> there must be at least a hundred packages in Debian for what you
> describe, from note taking to mind mappming to personal wikis.
>
> Don't abuse debian-science because you think of yourself as a scientist.

I don't agree that this constitutes "abuse" of debian-science.  This
list is for discussion of tools for scientific development, and a couple
of long threads have dealt with typesetting tools suited for science.
If typesetting is on-topic, why not data management?

That said, I'll echo the recommendation to use apt-cache search.

-Adam
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Engineering consulting with open source tools
http://www.opennovation.com/

[George N. White III]

On Mon, Jun 9, 2008 at 5:42 PM, Adam C Powell IV <hazelsct@...> wrote:

> On Mon, 2008-06-09 at 15:29 +0000, Dirk Eddelbuettel wrote:
>> This is a debian-user question.  Learn to use 'apt-cache search' --
>> there must be at least a hundred packages in Debian for what you
>> describe, from note taking to mind mappming to personal wikis.
>>
>> Don't abuse debian-science because you think of yourself as a scientist.
>
> I don't agree that this constitutes "abuse" of debian-science.  This
> list is for discussion of tools for scientific development, and a couple
> of long threads have dealt with typesetting tools suited for science.
> If typesetting is on-topic, why not data management?
>
> That said, I'll echo the recommendation to use apt-cache search.

The OP should consider one of the many systems (beagle, tracker,
namazu, ...) to maintain an index of a filestore.   Many will attempt to
extract terms from document formats (.tex. pdf, .doc, html, etc).  Also,
agrep is designed to improve on grep for searching text stores.


--
George N. White III <aa056@...>
Head of St. Margarets Bay, Nova Scotia


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